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Commit 7edc80c4 authored by sudorook's avatar sudorook
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clarify when to use OMP_NUM_THREADS

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......@@ -682,17 +682,21 @@ frequencies of the `21x21` pairs of amino acids at positions i and j.
__For users of shared resources:__ OpenMP will default to the number of
available cores, so if the bmDCA programs are run on a shared resource, say a
cluster, all cores will be engaged, starving other processes of resources or
causing the scheduler or cluster manager to boot you off the system. To prevent
this, use the `OMP_NUM_THREADS` environmental variable.
getting you booted off the system. To prevent this, use the `OMP_NUM_THREADS`
environmental variable.
You can either set it at runtime:
```
OMP_NUM_THREADS=4 bmdca -i ...
```
Or, you can set it globally, for example as shell run command.
Or, you can set it globally, for example in your shell rc file.
```
export OMP_NUM_THREADS=4
```
(The above examples will limit OpenMP to 4 threads.)
The above examples will limit OpenMP to 4 threads.
__You don't need to worry about this if submitting jobs through a workload
manager__, such as Slurm or Sun Grid Engine. The manager will limit bmDCA to
the number of cores specified, so manipulating `OMP_NUM_THREADS` is not needed.
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